The community of Rancho Peñasquitos is located west of Interstate 15, north of Los Peñasquitos Canyon Preserve, south of the community of Rancho Bernardo and east of the Torrey Highlands Community. State Route 56 traverses east-west through the central portion of the community. Rancho Peñasquitos encompasses approximately 6,500 acres including Black Mountain Regional Park.
The community has a diverse topography that is characterized by numerous canyons, hillsides and ridges. The most prominent feature of the community is Black Mountain which rises to an elevation of 1,500 feet.